5ZVD | pdb_00005zvd

The crystal structure of NSun6 from Pyrococcus horikoshii

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B [auth A]	PUA	e5zvdA2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: PUA	ECOD (1.6)
B [auth A]	Methyltr_RsmF_N	e5zvdA3	A: a+b two layers	X: Alpha-beta plaits	H: NOL1/NOP2/sun N-terminal ferredoxin-like domain (From Topology)	T: NOL1/NOP2/sun N-terminal ferredoxin-like domain	F: Methyltr_RsmF_N	ECOD (1.6)
B [auth A]	Methyltr_RsmB-F_1	e5zvdA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Methyltr_RsmB-F_1	ECOD (1.6)
A [auth B]	PUA	e5zvdB2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: PUA	ECOD (1.6)
A [auth B]	Methyltr_RsmF_N	e5zvdB3	A: a+b two layers	X: Alpha-beta plaits	H: NOL1/NOP2/sun N-terminal ferredoxin-like domain (From Topology)	T: NOL1/NOP2/sun N-terminal ferredoxin-like domain	F: Methyltr_RsmF_N	ECOD (1.6)
A [auth B]	Methyltr_RsmB-F_1	e5zvdB1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Methyltr_RsmB-F_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth A]	2.30.130.10	Mainly Beta	Roll	Archaeosine Trna-guanine Transglycosylase	Chain: A, domain 4	CATH (utative)
A [auth B]	2.30.130.10	Mainly Beta	Roll	Archaeosine Trna-guanine Transglycosylase	Chain: A, domain 4	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth B], B [auth A]	PF01472	PUA domain (PUA)	PUA domain	The PUA domain named after Pseudouridine synthase and Archaeosine transglycosylase, was detected in archaeal and eukaryotic pseudouridine synthases, archaeal archaeosine synthases, a family of predicted ATPases that may be involved in RNA modificatio ...	The PUA domain named after Pseudouridine synthase and Archaeosine transglycosylase, was detected in archaeal and eukaryotic pseudouridine synthases, archaeal archaeosine synthases, a family of predicted ATPases that may be involved in RNA modification, a family of predicted archaeal and bacterial rRNA methylases. Additionally, the PUA domain was detected in a family of eukaryotic proteins that also contain a domain homologous to the translation initiation factor eIF1/SUI1; these proteins may comprise a novel type of translation factors. Unexpectedly, the PUA domain was detected also in bacterial and yeast glutamate kinases; this is compatible with the demonstrated role of these enzymes in the regulation of the expression of other genes [1]. It is predicted that the PUA domain is an RNA binding domain.	Domain
A [auth B], B [auth A]	PF01189	16S rRNA methyltransferase RsmB/F (Methyltr_RsmB-F)	16S rRNA methyltransferase RsmB/F	This is the catalytic core of this SAM-dependent 16S ribosomal methyltransferase RsmB/F enzyme [1,2]. There is a catalytic cysteine residue at 180 in UniProtKB:Q5SII2, with another highly conserved cysteine at residue 230. It methylates the C(5) posi ...	This is the catalytic core of this SAM-dependent 16S ribosomal methyltransferase RsmB/F enzyme [1,2]. There is a catalytic cysteine residue at 180 in UniProtKB:Q5SII2, with another highly conserved cysteine at residue 230. It methylates the C(5) position of cytosine 2870 (m5C2870) in 25S rRNA [1,2].	Domain
A [auth B], B [auth A]	PF22458	Methyltr_RsmF/B-like, ferredoxin-like domain (RsmF-B_ferredox)	Methyltr_RsmF/B-like, ferredoxin-like domain	This entry represents a ferredoxin-like domain found in methyltransferases RsmB, RsmF and related sequences [1-5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B], B [auth A]	389aa long hypothetical nucleolar protein	tRNA methyltransferase activity RNA methyltransferase activity catalytic activity, acting on RNA tRNA (cytidine) methyltransferase activity transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA transferase activity S-adenosylmethionine-dependent methyltransferase activity tRNA (cytidine-5-)-methyltransferase activity methyltransferase activity catalytic activity RNA binding binding tRNA methyltransferase activity RNA methyltransferase activity catalytic activity, acting on RNA tRNA (cytidine) methyltransferase activity transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA transferase activity S-adenosylmethionine-dependent methyltransferase activity tRNA (cytidine-5-)-methyltransferase activity methyltransferase activity catalytic activity RNA binding binding tRNA binding nucleic acid binding	tRNA modification RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process RNA modification biosynthetic process tRNA processing macromolecule modification tRNA modification RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process RNA modification biosynthetic process tRNA processing macromolecule modification metabolic process cellular process macromolecule metabolic process RNA processing macromolecule methylation methylation RNA methylation	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B], B [auth A]	IPR015947	PUA-like superfamily	Homologous Superfamily
A [auth B], B [auth A]	IPR054728	Ribosomal RNA small subunit methyltransferase B-like, ferredoxin-like domain	Domain
A [auth B], B [auth A]	IPR004521	Uncharacterised domain CHP00451	Domain
A [auth B], B [auth A]	IPR001678	SAM-dependent methyltransferase RsmB-F/NOP2-type domain	Domain
A [auth B], B [auth A]	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A [auth B], B [auth A]	IPR023267	RNA (C5-cytosine) methyltransferase	Family
A [auth B], B [auth A]	IPR011023	Nop2p	Domain
A [auth B], B [auth A]	IPR036974	PUA domain superfamily	Homologous Superfamily
A [auth B], B [auth A]	IPR043699	tRNA (cytosine(72)-C(5))-methyltransferase	Family
A [auth B], B [auth A]	IPR002478	PUA domain	Domain
A [auth B], B [auth A]	IPR049560	SAM-dependent methyltransferase RsmB-F/NOP2-type, catalytic core	Domain

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.